[go: up one dir, main page]

EP1826279B1 - Détection et contrôle de la qualité de lymphocytes T de régulation via l'analyse de méthylation de l'ADN du gène FoxP3 - Google Patents

Détection et contrôle de la qualité de lymphocytes T de régulation via l'analyse de méthylation de l'ADN du gène FoxP3 Download PDF

Info

Publication number
EP1826279B1
EP1826279B1 EP07004186A EP07004186A EP1826279B1 EP 1826279 B1 EP1826279 B1 EP 1826279B1 EP 07004186 A EP07004186 A EP 07004186A EP 07004186 A EP07004186 A EP 07004186A EP 1826279 B1 EP1826279 B1 EP 1826279B1
Authority
EP
European Patent Office
Prior art keywords
seq
cells
foxp3
regulatory
positions
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Active
Application number
EP07004186A
Other languages
German (de)
English (en)
Other versions
EP1826279A1 (fr
Inventor
Jochen Hühn
Stefan Flöss
Alf Hamann
Sven Olek
Udo Baron
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Charite Universitaetsmedizin Berlin
Precision for Medicine GmbH
Original Assignee
Charite Universitaetsmedizin Berlin
Epiontis GmbH
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Charite Universitaetsmedizin Berlin, Epiontis GmbH filed Critical Charite Universitaetsmedizin Berlin
Priority to PL07004186T priority Critical patent/PL1826279T3/pl
Priority to SI200730679T priority patent/SI1826279T1/sl
Publication of EP1826279A1 publication Critical patent/EP1826279A1/fr
Application granted granted Critical
Publication of EP1826279B1 publication Critical patent/EP1826279B1/fr
Active legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Images

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/118—Prognosis of disease development
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/154—Methylation markers

Definitions

  • the present invention relates to an in vitro method for detecting FoxP3 positive CD25 + CD4 + regulatory T cells of a mammal, comprising analysing the methylation status of at least one CpG position in the 5' region upstream from the transcription start, promoter regions, introns, and/or exon/intron borders of the gene foxp3 or an orthologous or paralogous gene thereof. Furthermore, the present invention relates to a kit for performing the above methods as well as respective uses.
  • Regulatory T cells play an important role for the maintenance of immunological tolerance by suppressing the action of autoreactive effector cells, making them interesting targets for therapeutic applications. Therefore, these cells are critically involved in preventing the development of autoimmune reactions ( Sakaguchi, Nat Immunol 6:345-352, 2005 ).
  • the transcription factor Foxp3 is specifically expressed in regulatory T cells and is thought to function as a master switch for the development and function of these cells. Recently, it has been demonstrated that ectopic expression of Foxp3 in conventional T cells confers suppressive activity ( Fontenot and Rudensky, Nat Immunol 6:331-337, 2005 ).
  • Foxp3 + regulatory T cells arise from conventional T cells both in vitro and in vivo upon antigen recognition under tolerogenic conditions. In all cases the expression of Foxp3 is characteristic for the development of regulatory T cells.
  • WO 02/090600 describes isolated nucleic acid molecules which encode Fkhsf, as well as mutant forms thereof. Also described are expression vectors suitable for expressing such nucleic acid molecules, and host cells containing such expression vectors. Also described are pharmaceutical compounds and methods of identifying such compounds that can modulate the immune system. In addition are provided methods for identifying proteins regulated by Scurfin and proteins that induce or inhibit Foxp3 expression.
  • EP-A-1 213 360 describes materials for the generation of methylation fingerprints of particular cells.
  • WO2004/050706 discloses the expression phenotypes of regulatory T-cells.
  • One phenotype is defined by the combined expression of FoxP3 in addition to CD4, CD25, and CCR5.
  • the analyses are based on FACS and/or antibody analysis.
  • US2003/170648 discloses a method for identifying a compound that modulates the level of expression of scurfin (FoxP3) using a a reporter gene ligated to a scurfin promoter in the background of a mutated foxP3 gene.
  • the primary target of methylation is the two-nucleotide sequence Cytosine-Guanine (a 'CpG site'); within this context cytosine (C) can undergo a simple chemical modification to become 5-methyl-cytosine.
  • C Cytosine-Guanine
  • the CG sequence is much rarer than expected except in certain relatively dense clusters called 'CpG islands'.
  • CpG islands are frequently associated with gene promoters, and it has been estimated that more than half of the human genes have CpG islands ( Antequera and Bird, Proc Natl Acad Sci U S A. 90:11995-9, 1993 ).
  • Methylation profiles have been recognised to be tumour specific (i.e., changes in the methylation pattern of particular genes or even individual CpGs are diagnostic of particular tumour types) and there is now an extensive collection of diagnostic markers for bladder, breast, colon, oesophagus, stomach, liver, lung, and prostate cancers (summarised by Laird, Nature Reviews/Cancer 3:253-266, 2003 ).
  • Epigenetic control by methylation is essential for early development including embryogenesis, X-chromosome inactivation and imprinting (monoallelic silencing) of either the paternal or maternal allele ( Erlich, J Cellular Chem 88:899-910, 2003 ).
  • Tissue-specific methylation also serves in regulating adult cell types/stages, and in some cases a causal relationship between methylation and gene expression has been established.
  • methylation may be a by-product of some other primary regulation, or it is required to lock the gene in the "off" state ( Erlich, J Cellular Chem 88:899-910, 2003 ).
  • a causal relationship is not required, merely a strong correlation between methylation patterns and cell types.
  • helper T cells helper T cells
  • IFN- ⁇ Interferon-gamma
  • Th2 produces IL-4 and silences IFN- ⁇
  • the IFN- ⁇ promoter is methylated, but not in Th1 cells where IFN- y is expressed ( Attwood et al., CMLS 59:241-257, 2002 ). Conversely, the entire transcribed region of IL-4 becomes demethylated under Th2-inducing conditions, which strongly correlates with efficient transcription of IL-4. In Th1 cells, this extensive demethylation does not occur, rather particular untranscribed regions gradually become heavily methylated and IL-4 is not expressed ( Lee et al., Immunity 16:649-660, 2002 ). Furthermore, Bruniquel and Schwartz (Nat Immunol.
  • the present invention solves the above object by providing a method for detecting FoxP3-positive stable CD25 + CD4 + regulatory T cells of a mammal, comprising analysing the methylation status of at least one CpG position in the 5' region upstream from the transcription start, promoter regions, introns, and/or exon/intron borders of the gene foxp3 or an orthologous or paralogous gene thereof. Said method is performed in vitro.
  • the analysis of the accessibility of the Foxp3 locus provides additional information, besides the mere expression of Foxp3, to what extent a permanent conversion into a regulatory T cell lineage has occurred (see also below in the context of TGF- ⁇ -induced regulatory T cells).
  • the inventors have identified a particular region within the Foxp3 gene, which are functionally involved in the regulation of stable Foxp3 expression in regulatory T cells.
  • This region contains many CpG motifs, which display a differential methylation status when cells expressing Foxp3 (preferably CD25 + CD4 + ) compared with cells not expressing Foxp3 (preferably CD25 - CD4 + ), if, for example, the bisulphite sequencing method is used.
  • the inventors could demonstrate that in Foxp3 + cells the CpG motifs are almost completely demethylated (i.e. to more than 70%, preferably 80%, preferably, more than 90% and most preferred more than 95%), whereas the same motifs are completely methylated in Foxp3 - cells.
  • the lymphoproliferative disorder of scurfy mice is completely rescued by transgenic complementation with a 30.8-kb genomic fragment containing the Foxp3 gene from wild type mice ( Brunkow ME, Jeffery EW, Hjerrild KA, Paeper B, Clark LB, Yasayko SA, Wilkinson JE, Galas D, Ziegler SF, Ramsdell F. Disruption of a new forkhead/winged-helix protein, scurfin, results in the fatal lymphoproliferative disorder of the scurfy mouse. Nat Genet. 2001 Jan;27(1):68-73 .).
  • the term "gene” shall mean a region of the chromosomal DNA that encodes for a certain protein, such as FoxP3, and contains other genetic elements that are responsible for the regulation of said gene.
  • a gene includes also introns, enhancers, promoter sequences and the 5' untranslated region of the gene.
  • the gene will not only include the sequence as given in Brunkow et al. ( Brunkow ME, Jeffery EW, Hjerrild KA, Paeper B, Clark LB, Yasayko SA, Wilkinson JE, Galas D, Ziegler SF, Ramsdell F.
  • Homo sapiens FoxP3 (forkhead box P3) is therefore an ortholog of the Mus musculus Foxp3 (forkhead box P3) gene and/or protein.
  • Other orthologs are C. familiaris LOC491876 (similar to Forkhead box protein P3), and R. norvegicus LOC317382 (similar to scurfin).
  • "Paralogs" are genes related by duplication within a genome and are also called a paralogous gene. Orthologs retain the same function in the course of evolution, whereas paralogs evolve new functions, even if these are related to the original one.
  • paralog is a "pseudogene” that is a nucleotide sequences that is similar to a normal gene, but does not produce a functional final product.
  • pseudogene a nucleotide sequences that is similar to a normal gene, but does not produce a functional final product.
  • pseudogenes There are two variants of pseudogenes. The first requires the final product to be a protein. The second allows the final product to be an RNA.
  • the person of skill will be readily able, to compare the orthologous or paralogous genes (for example using a computer program in order to align the sequences, such as the fasta program), and to identify regions and/or CpG positions that can be found in the same regions and/or even at the same equivalent positions in the (both) genes. According to the present invention, these regions and/or CpG positions are regarded as orthologous or paralogous.
  • an alignment is based on the level of sequence identity between the two (or more) DNA fragments that are analyzed.
  • a 384-bp stretch that is differentially methylated in the region as covered by amplicons 1 and 2 (as described herein), but not the region covered by amplicons 3 and 4 is highly conserved between mice and men (80.7% sequence identity), suggesting that in both mammals functionally important parts can be found that are both subject to epigenetic regulation.
  • the Treg-specific demethylated region could be identified.
  • Other levels of sequence identity are preferably about 75%, more preferably about 80%, and most preferred about 90% of a given fragment.
  • said analysis of the methylation status comprises amplification with at least one of the primer pairs selected from SEQ ID No. 1 and 2; SEQ ID No. 3 and 4; SEQ ID No. 5 and 6; SEQ ID No. 7 and 8, SEQ ID No. 9 and 10; SEQ ID No. 11 and 12; SEQ ID No. 13 and 14; SEQ ID No. 15 and 16; SEQ ID No. 17 and 18; SEQ ID No. 19 and 20; SEQ ID No. 21 and 22; SEQ ID No. 23 and 24; SEQ ID No. 25 and 26; SEQ ID No. 27 and 28; SEQ ID No. 29 and 30, and orthologous or paralogous primer pairs thereof.
  • the amplification involves a polymerase enzyme, a PCR or chemical amplification reaction, or other amplification methods as known to the person of skill as described below, e.g. in the context of MSP, HeavyMethyl, or MethyLight.
  • amplicons 1 to 4 or human amplicans 1 to 11 (as described herein) or orthologs or paralogs thereof are produced that are particularly preferred "tools" for performing the method(s) according to the present invention. Consequently, an oligomer according to any of SEQ ID No. 1 to 30 or an amplicon as amplified by a primer pair selected from SEQ ID No. 1 and 2; SEQ ID No. 3 and 4; SEQ ID No.
  • orthologous or paralogous primer pairs can be designed by the person of skill having a sequence identity with the above primers of preferably about 75%, more preferably about 80%, and most preferred about 90%. Particularly preferred is a method according to the present invention, wherein said analysis of the methylation status comprises amplification with at least one of the primer pairs selected from SEQ ID No. 1 and 2; SEQ ID No. 3 and 4; SEQ ID No. 15 and 16; SEQ ID No. 17 and 18, SEQ ID No. 19 and 20; SEQ ID No. 21 and 22; SEQ ID No. 23 and 24; SEQ ID No. 29 and 30; and orthologous or paralogous primer pairs thereof.
  • the analysis of the methylation status comprises analysing the methylation status of at least one CpG position selected from the group consisting of nucleotide positions 38, 74, 90, 124, 151, 156, 205, 224, 228, 236, 298, and 368 of the amplicon 2 as amplified by the primer pair SEQ ID No. 1 and 2, nucleotide positions 158, 180, 308, 344, 360, 394, 421, and 426 of the amplicon 1 as amplified by the primer pair SEQ ID No.
  • said analysis of the methylation status comprises analysing the methylation status of at least one CpG position selected from the group consisting of positions 38, 74, 90, 124, 156, 205, 224, 236, 298, and 368 of the amplicon 2 as amplified by the primer pair SEQ ID No. 1 and 2, positions 180, 308, 344, and 394 of the amplicon 1 as amplified by the primer pair SEQ ID No. 3 and 4, and orthologous or paralogous CpG positions thereof. It could be shown in the experiments that these positions were mostly demethylated in the regulatory T cells.
  • the person of skill will furthermore be able to select specific subsets of CpG positions in order to minimise the amount of sites to be analyzed, for example all sites as present on amplicon 1 or all sites as present on amplicon 2 or orthologous or paralogous CpG positions thereof.
  • the analysis of the methylation status comprises a method selected from methylation specific enzymatic digests, bisulphite sequencing, analysis selected from promoter methylation, CpG island methylation, MSP, HeavyMethyl, MethyLight, Ms-SNuPE or other methods relying on a detection of amplified DNA.
  • the method according to the present invention can be performed with any mammal having the foxp3 gene or an ortholog or paralog thereof, preferred is a method according to the present invention, wherein said mammal is a mouse, rat, monkey or human.
  • the method according to the present invention further comprises an induction with TGF- ⁇ .
  • TGF- ⁇ A critical issue for application of regulatory T cells in therapeutical approaches is the availability of large numbers of cells.
  • Recent publications have reported that conventional CD25 - CD4 + T cells can be converted into Foxp3 + regulatory T cells by stimulation in presence of TGF- ⁇ ( Chen W, Jin W, Hardegen N, Lei KJ, Li L, Marinos N, McGrady G, Wahl SM. Conversion of peripheral CD4+CD25- naive T cells to CD4+CD25+ regulatory T cells by TGF-beta induction of transcription factor Foxp3. J Exp Med.
  • a method for diagnosing the immune status of a mammal comprising the steps of a) obtaining a sample containing T-cells from said mammal to be diagnosed, b) analysing the methylation status of at least one CpG position in the gene foxp3 or an orthologous or paralogous gene thereof according to the present invention in said T-cells, c) identifying the amount of regulatory T-cells present in said sample based on said methylation status, and d) concluding on the immune status of said mammal based on said amount as identified.
  • the method can be performed with any mammal having the foxp3 gene or an ortholog or paralog thereof, preferred is a method according to the present invention, wherein said mammal is a mouse, rat, monkey or human. Preferred is a method, wherein said mammal is a patient suffering from a disease selected from autoimmune diseases, adverse effects in allotransplantate recipients, tumorous diseases, ovarian cancer, chronic graft-versus-host disease, allergic asthma, multiple sclerosis, and IPEX syndrome. These diseases have already been described herein.
  • the amount of regulatory T-cells corresponds to a demethylation of the CpG positions as analyzed to at least 80%, preferably 90%, and more preferably 95%.
  • a method that is further comprising measuring and/or monitoring the amount or ratio of said regulatory T cells in response to chemical and/or biological substances that modulate foxp3 expression in the regulatory T cell. That is, changes in the amount or ratio of regulatory T cells that are caused by, for example, the treatment of a disease (e.g. as described herein), and the success and/or progress of said treatment in terms of an effect on regulatory T cells can be followed using this method.
  • a follow-up of the methylation pattern of T cells based on the marker herein will point to changes in the cells that are due to a response to said chemical and/or biological substances, in some cases even before a phenotypic change can be observed.
  • a method for determining the suitability of in vitro generated or expanded regulatory T cells for a transfer into a patient comprising the method according to the present invention, and detecting, whether the CpG positions as analyzed are demethylated to at least 80%, preferably 90%, and more preferably 95%.
  • the method can be performed in vitro and/or in vivo.
  • T cells that appear to show a modified, in particular a drop, of foxp3 expression are usually not regarded as stable and will not be used further.
  • the present invention provides a method for identifying chemical and/or biological substances that modulate foxp3 expression in a T cell, comprising contacting one or more of said chemical and/or biological substance with a T cell, performing the method according to the present invention as described above, and detecting, whether said chemical and/or biological substance modulates methylation of the CpG positions as analyzed.
  • the method is performed in vitro.
  • the present invention encompasses a method, sometimes called a "screening-method", that seeks to identify chemical and/or biological substances modulating foxp3 expression that can be used as starting points for the development of regulatory T cell specific medication and respective pharmaceutical compositions.
  • the present method is based on the fact that it is well accepted that the foxp3 gene plays a central role for the development of regulatory T cells. Therefore, factors modulating Foxp3 expression are also interesting tools to treat autoimmune diseases or allotransplantate recipients. Even factors preventing Foxp3 expression are interesting for the treatment of tumour patients, where Foxp3 + regulatory T cells have been shown to prevent a strong anti tumour response. Such factors, which lead to a stable modification of Foxp3 expression, can be detected with the method described in this invention. Furthermore, factors that can enhance the differentiation of regulatory T-cells and lead to an alleviation of autoimmune and allergenic disorders can be identified with the present method.
  • Chemical and/or biological substances that are suitable as screening compounds are known to the person of skill and, for example, include small molecules, peptides and proteins, and antibodies or fragments thereof. Furthermore, the screening can be done using a commercially compound library, optimally together with suitable automation, such as a robot. In one preferred embodiment of the method for identifying chemical and/or biological substances, said substance provides a demethylation of the CpG positions as analyzed to at least 80%, preferably 90%, and more preferably 95%.
  • FoxP3 The expression of FoxP3 is described as being associated with poor prognosis in ovarian cancer ( Wolf, D., et al. The expression of the regulatory T cell-specific forkhead box transcription factor FoxP3 is associated with poor prognosis in ovarian cancer. Clin. Cancer Res. 11 (23), 8326-8331 (2005 )). High expression levels of FoxP3 are associated with ovarian cancer. Furthermore, the gene expression of regulatory T cells transcription factor FOXP3 was reduced in chronic graft-versus-host disease patients ( Zorn, E., et al. Reduced frequency of FOXP3+ CD4+CD25+ regulatory T cells in patients with chronic graft-versus-host disease.
  • foxp3 is the only gene currently known to be associated with IPEX syndrome. Approximately 60% of males with IPEX syndrome have mutations identified in the foxp3 gene.
  • foxp3 was furthermore linked to autoimmune diseases such as multiple sclerosis (MS) ( Huan J, Culbertson N, Spencer L, Bartholomew R, Burrows GG, Chou YK, Bourdette D, Ziegler SF, Offner H, Vandenbark AA. Decreased FOXP3 levels in multiple sclerosis patients. J Neurosci Res. 2005 Jul 1;81(1):45-52 .).
  • MS multiple sclerosis
  • foxp3 expression clearly establish a connection between foxp3 expression and autoimmune diseases, adverse effects in allotransplantate recipients, tumorous diseases, ovarian cancer, chronic graft-versus-host disease, allergic asthma, and IPEX syndrome.
  • a method for the diagnosis of diseases that are associated with the aberrant expression of the gene foxp3, comprising the method according to the present invention, and detecting, whether the CpG positions as analyzed are demethylated to at least 80%, preferably 90%, and more preferably 95%, wherein the diseases are selected from autoimmune diseases, adverse effects in allotransplantate recipients, tumorous diseases, ovarian cancer, chronic graft-versus-host disease, allergic asthma, and IPEX syndrome.
  • the present method can be performed in vitro and/or in vivo, and allows for a more specific determination of the parameter FoxP3, as temporary expression of FoxP3, especially in the human system, has been detected also in activated, non-regulatory T cells ( Ziegler SF. FOXP3: Of Mice and Men. Annu Rev Immunol. 2005 Dec 1 ).
  • kits for identifying regulatory T cells based on the analysis of the methylation status of CpG positions in the gene foxp3, comprising materials for performing a method according to the present invention.
  • the kit comprises a) a bisulfite reagent, and b) materials for the methylation analysis of CpG positions selected from the positions consisting of positions 38, 74, 90, 124, 156, 205, 224, 236, 298, and 368 of the amplicon 2 as amplified by the primer pair SEQ ID No. 1 and 2, positions 180, 308, 344, and 394 of the amplicon 1 as amplified by the primer pair SEQ ID No.
  • the kit can be a diagnostic kit.
  • kits according to the present invention may also contain: 1. Chemicals (bisulfite, etc.) for processing the cell samples; 2. Procedure protocols; 3. Oligonucleotide probes, amplicons, blockers or extension primers according to the present invention that will detect markers relevant to a particular cell type.
  • the oligonucleotides would be constructed to generate a signal on a commonly available detection platform, such as Real Time-PCR (RT-PCR) or Single Base Extension (SBE). Each signal indicates the level of methylation at a particular target site in the sample.
  • RT-PCR Real Time-PCR
  • SBE Single Base Extension
  • Each signal indicates the level of methylation at a particular target site in the sample.
  • probes according to the described nucleic acids could be produced for usage on a chip; 4.
  • Yet another preferred aspect of the present invention relates to the use of a kit according to the present invention for detecting and/or identifying FoxP3-positive regulatory T cells, preferably CD25 + CD4 + regulatory T cells, in analogy to what has been described above.
  • Described herein is a method of treatment of diseases that are related to Foxp3 expression, such as autoimmune diseases, adverse effects in allotransplantate recipients, tumorous diseases, ovarian cancer, chronic graft-versus-host disease, allergic asthma, multiple sclerosis, and IPEX syndrome.
  • the method comprises administering an effective amount of stable FoxP3-positive regulatory T cells, preferably CD25 + CD4 + regulatory T cells to said patient in need thereof.
  • stable FoxP3-positive regulatory T cells preferably stable CD25 + CD4 + regulatory T cells is described in the literature (for example in Bharat A, Fields RC, Mohanakumar T. Regulatory T cell-mediated transplantation tolerance. Immunol Res. 2006;33(3):195-212 .
  • the analysis of the methylation status of the region within the foxp3 locus allows an improved prediction whether the cell population will stably express the FoxP3 gene or not. Therefore, this method can be used as a quality control for in vitro generated or expanded regulatory T cells before adoptive transfer into patients which suffer from autoimmune diseases or which have received an allotransplant. Only if the CpG motifs are demethylated to a certain degree it is confident that these cells will stably express the Foxp3 gene and will not loose foxp3 expression after some period of time. This scenario would have a fatal outcome since the adoptively transferred cells could convert from Foxp3 + regulatory T cells into pathogenic effector cells, which might lead to a worsening of the disease state. Therefore, a quality control concerning the stability of the regulatory phenotype of adoptively transferred cells is absolutely required and can be achieved by the analysis of the methylation status of the aforementioned region of the Foxp3 locus.
  • the methylation status of the Foxp3 locus was analyzed by bisulphite sequencing and revealed striking differences between CD25 + CD4 + regulatory T cells and conventional CD25 - CD4 + T cells.
  • Amplicons 1 and 2 displayed a high degree of methylation (nearly 100%) within conventional CD25 - CD4 + T cells, but were almost completely demethylated within CD25 + CD4 + regulatory T cells ( Figure 3 ). No differences were observed for amplicons 3 and 4 showing that the demethylation process is not a random event, but confined to defined regions as was recently found for the IL-2 promoter ( Bruniquel D, Schwartz RH. Selective, stable demethylation of the interleukin-2 gene enhances transcription by an active process. Nat Immunol.
  • the above region appears to be particularly involved in the regulation of foxp3, maybe in form of an alternative TATA-less promoter (the TATA box can be found upstream of the amplicons). Furthermore, there appears to be alternative splicing in the foxp3 gene (Genebank Accession number DQ010327).
  • CD25 + but not CD25 - CD4 SP thymocytes displayed demethylated CpG motifs within the regions covered by amplicons 1 and 2. Again, CpGs in amplicons 3 and 4 were equally methylated.
  • CD25 + CD4 SP thymocytes showed a slightly reduced degree of demethylated DNA within amplicons 1 and 2 when compared to peripheral CD25 + CD4 + regulatory T cells.
  • Intracellular FOXP3 staining of FACS-sorted subsets revealed specific FOXP3 expression only in CD25highCD45RA-CD4+ Tregs ( Figure 5A ), in accordance with findings from other labs ( Walker MR, Kasprowicz DJ, Gersuk VH, Benard A, Van Landeghen M, Buckner JH, Ziegler SF. Induction of FoxP3 and acquisition of T regulatory activity by stimulated human CD4+CD25- T cells. J Clin Invest. 2003;112:1437-1443 .
  • CpGs were found to be methylated in both cell types in the 3' region of the gene (Amps 1 and 2 in Figure 5B ). Upstream of exon -1, CpGs in both cell types were demethylated up to the 5' end of a CpG island (Amps 9 and 10). At the 5' end of the FOXP3 gene, methylation was observed only in naive CD4+ T cells, while tending towards demethylation in Tregs (Amps 10 and 11). Striking differences in the methylation pattern were observed within the gene body and putative promoter regions (Amps 3-8), in particular in a region highly conserved between mammals (Amp 5), for which we propose the name TSDR (Treg-specific demethylated region). To verify this finding, the inventors analyzed the methylation pattern of TSDR in another 12 donors (donors # 4-15).
  • Transient FOXP3 expression in the absence of regulatory function has recently been reported for activated conventional CD4+ T cells ( Morgan ME, van Bilsen JH, Bakker AM, Heemskerk B, Schilham MW, Hartgers FC, Elferink BG, van der Zanden ,L de Vries RR, Huizinga TW, Ottenhoff TH, Toes RE.
  • Expression of FOXP3 mRNA is not confined to CD4+CD25+ T regulatory cells in humans.
  • Hum Immunol. 2005;66:13-20 Gavin MA, Torgerson TR, Houston E, Deroos P, Ho WY, Stray-Pedersen A, Ocheltree EL, Greenberg PD, Ochs HD, Rudensky AY.
  • the cells upon stimulation, not only uniformly upregulated both CD25 and FOXP3, but also expressed high levels of FOXP3 (FOXP3high) in a significant fraction of cells ( Figure 7 , Table 2), confirming recently published data ( Morgan ME, van Bilsen JH, Bakker AM, Heemskerk B, Schilham MW, Hartgers FC, Elferink BG, van der Zanden ,L de Vries RR, Huizinga TW, Ottenhoff TH, Toes RE.
  • the bisulfite sequencing analysis of representative gene regions showed various differentially methylated regions including - but not limited to - the TSDR (Treg-specific demethylated region).
  • TSDR Teg-specific demethylated region
  • the data of freshly isolated na ⁇ ve T cells and Tregs confirm previously reported murine data36, underlining the outstanding significance of this differentially methylated region.
  • mice were bred at the BfR (Bundesinstitut fuer Nutritionbeêt, Berlin, Germany) and used at 6-12 wk of age. All animal experiments were performed under specific pathogenfree conditions and in accordance with institutional, state and federal guidelines.
  • CD4 + T cells were isolated from pooled spleen and LN single cell suspensions by using anti CD4-FITC plus anti FITC multisort microbeads and the AutoMACS magnetic separation system (Miltenyi Biotec). After release of beads according to the manufacturer's instructions, CD25 + and CD25 - cells were separated using anti CD25-APC plus anti APC microbeads. Thymic single cell suspensions were sorted for CD8 + and CD8 - cells using anti CD8 microbeads and the AutoMACS magnetic separation system.
  • MACS-sorted CD8 - thymocytes were subsequently stained using anti CD4-FITC, anti CD25-APC and anti CD19-PE and sorted into CD25 + and CD25 - subsets of CD4 SP thymocytes as well as into CD19 - DN thymocytes by FACS (Aria, BD Bioscience).
  • MACS-sorted CD8 + thymocytes were stained using anti CD4-FITC and anti CD8-PerCP and sorted into DP thymocytes by FACS. All subsets were sorted to a purity of >98%.
  • CD4 + T cells were isolated from pooled spleen and LN single cell suspensions by using anti CD4-FITC plus anti FITC multisort microbeads and the AutoMACS magnetic separation system (Miltenyi Biotec). After release of beads according to the manufacturer's instructions, CD25 + cells were depleted by using anti CD25 - APC plus anti APC microbeads. To avoid the expansion of precommitted Foxp3 + regulatory T cells the inventors excluded the majority of residual Foxp3 + regulatory T cells from the CD25 - CD4 + T cell fraction by sorting for CD62Lhigh cells using anti CD62L microbeads.
  • MACS-sorted CD62LhighCD25 - CD4 + T cells were stimulated for 2 days using plate bound anti CD3 (6 ⁇ g/ml) and anti CD28 (4 ⁇ g/ml).
  • plate bound anti CD3 6 ⁇ g/ml
  • anti CD28 4 ⁇ g/ml
  • For Th1 cultures 5 ⁇ g/ml anti-IL-4, 20 ng/ml IFN- ⁇ (R&D systems) and 5 ng/ml IL-12 (R&D systems) and for TGF- ⁇ cultures 5 ng/ml TGF- ⁇ (Sigma) and 10 ng/ml IL-2 (R&D systems) was added to the culture. After 2 days cells were removed from the stimulus, transferred to non-coated plates and cultured for another 3 days. All cell culture was done with RPMI 1640 (Gibco) supplemented with 10% FCS (Sigma). On day 5, cultured cells were stained using anti CD25-APC and sorted for CD25+ cells by FACS (Aria).
  • the primers were used for both PCR amplification of bisulfite converted genomic DNA and sequence reactions.
  • Genomic DNA was isolated from purified lymphocytes using the DNeasy tissue kit (Qiagen, Hilden, Germany) following the supplier's recommendations.
  • PCRs were performed on MJ Research thermocyclers (Waltham, Massachusetts, United States) in a final volume of 25 ⁇ l containing 1x PCR Buffer, 1 U Taq DNA polymerase (Qiagen, Hilden, Germany), 200 ⁇ M dNTPs, 12.5 pmol each of forward and reverse primers, and 7 ng of bisulfite-treated genomic DNA.
  • the amplification conditions were 95 °C for 15 min and 40 cycles of 95 °C for 1 min., 55 °C for 45 sec and 72 °C for 1 min. and a final extension step of 10 min. at 72 °C.
  • PCR products were purified using ExoSAP-IT (USB Corp., Cleveland, Ohio, United States) and sequenced applying the PCR primer(s) and the ABI Big Dye Terminator v1.1 cycle sequencing chemistry (Applied Biosystems, Foster City, California, United States) followed by capillary electrophoresis on an ABI 3100 genetic analyzer. Trace files were interpreted using ESME, which normalizes sequence traces, corrects for incomplete bisulfite conversion and allows for quantification of methylation signals ( Lewin, J., Schmitt, A.O., Adorjan, P., Hildmann, T., Piepenbrock, C. (2004) Bioinformatics. 20, 3005-3012 ).
  • Buffy coats were obtained in accordance with local ethical committee approval (DRK Blutspendedienst, Berlin, Germany).
  • PBMCs were separated with a Ficoll-Hypaque gradient (Sigma-Aldrich). The purity of the sorted population was 95-99%, as determined by FACScalibur TM using CELLQest TM Software (BDBiosciences).
  • CD4+ T cells were isolated from PBMCs by using anti-CD4 microbeads and the AutoMACS magnetic separation system (Miltenyi Biotec). MACS-sorted CD4+ T cells were stained using anti-CD45RA-FITC and anti-CD25-APC (MA-251, BD-PharMingen).
  • FACS-sorted naive CD4+ T cells (CD25-CD45RA+) were stimulated for three to seven days using antiCD3/antiCD28-coated beads (Dynal) according to the manufacturers instructions.
  • Cell culture was performed in RPMI medium (Gibco) supplemented with 10% FCS (Sigma). On indicated time points, stimulated cells were harvested and aliquots were taken for both the analysis of FOXP3 expression by flow cytometry and for the analysis of the methylation status of the FOXP3 gene.
  • Genomic DNA was isolated using the DNeasy tissue kit (Qiagen) following the protocol for cultured animal cells. Bisulfite treatment of genomic DNA was performed as previously described ( Olek A, Oswald J, Walter J. A modified and improved method for bisulphite based cytosine methylation analysis Nucleic Acids Res. 2007;24:5064-5066 .).
  • PCRs were performed in a final volume of 25 ⁇ l containing1x PCR Buffer, 1U Taq DNA polymerase (Qiagen), 200 ⁇ M dNTPs, 12.5pmol each of forward and reverse primers, and 7ng of bisulphite-treated genomic DNA at 95°C for 15min and 40 cycles of 95°C for 1min, 55°C for 45sec and 72°C for 1min and a final extension step of 10min at 72°C.
  • PCR products were purified using ExoSAP-IT (USB Corp.) and sequenced applying the PCR primers and the ABI Big Dye Terminator v1.1-chemistry (Applied Biosystems) followed by capillary electrophoresis on an ABI 3100 genetic analyzer.
  • MS-SNuPE was performed using the ABIPrism-Snapshot kit (Applied Biosystems). Substrates were PCR products produced from bisulphite-converted genomic DNA using primers Amp5 "p" and "o". The assay utilizes internal extension primer(s) annealing immediately 5' of the relevant nucleotide. In presence of labelled ddNTPs, the primer is extended by a single nucleotide. Capillary Electrophoresic analysis was performed by using ABI 3100 Genetic Analyzer and GeneMapper software (v3.5). Extension primers: FOXP3: CCCAACAAACAATACAAAAAACC (SEQ Id. No.
  • Table 1 Demethylation of the FOXP3 gene in CD25highCD4+ Tregs corresponds to frequency of FOXP3+ cells.
  • MS-SNuPE analysis was performed as described in Figure 6 . Frequencies of unmethylated cytosins and frequencies of FOXP3+ cells within CD25highCD45RA- Tregs from male (M) and female (F) donors are depicted. Table 2: Methylated FOXP3 gene in activated conventional FOXP3+CD4+ T cells.
  • MS-SNuPE Summary of MS-SNuPE and flow cytometry analysis of in vitro stimulated naive CD4+ T cells from five donors. Cells were stimulated for varying time points. MS-SNuPE analysis was performed essentially as described in Figure 3 . Frequencies of unmethylated cytosins and frequencies of FOXP3 high cells within stimulated T cells from male (M) and female (F) donors are depicted.

Landscapes

  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Pathology (AREA)
  • Immunology (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Engineering & Computer Science (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • General Health & Medical Sciences (AREA)
  • Microbiology (AREA)
  • Biotechnology (AREA)
  • Oncology (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biochemistry (AREA)
  • Molecular Biology (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Hospice & Palliative Care (AREA)
  • Animal Behavior & Ethology (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Medicinal Chemistry (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Public Health (AREA)
  • Veterinary Medicine (AREA)
  • General Chemical & Material Sciences (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)

Claims (12)

  1. Procédé de détection de cellules T régulatrices CD25+CD4+ stables FoxP3+ d'un mammifère dans un échantillon obtenu dudit mammifère, comprenant le fait
    d'analyser l'état de méthylation d'au moins une position CpG dans la région 5' en amont de l'initiation de transcription, la région 5' non traduite, la région promotrice, les introns, et/ou les bordures intron/exon du gène Foxp3 ou d'un gène orthologue ou paralogue, correspondant
    où l'hypométhylation indique une cellule T régulatrice CD25+CD4+ stable FoxP3+.
  2. Procédé selon la revendication 1, dans lequel ladite analyse de l'état de méthylation comprend une amplification avec au moins l'une des paires d'amorces sélectionnées parmi SEQ ID n° 1 et 2 ; SEQ ID N° 3 et 4 ; SEQ ID N° 5 et 6 ; SEQ ID n° 7 et 8, SEQ ID N° 9 et 10 ; SEQ ID N° 11 et 12 ; SEQ ID N° 13 et 14 ; SEQ ID N° 15 et 16 ; SEQ ID N° 17 et 18 ; SEQ ID N° 19 et 20 ; SEQ ID N° 21 et 22 ; SEQ ID N° 23 et 24 ; SEQ ID N° 25 et 26 ; SEQ ID N°. 27 et 28 ; SEQ ID N° 29 et 30, et leurs paires d'amorces orthologues ou paralogues.
  3. Procédé selon la revendication 2, dans lequel ladite analyse de l'état de méthylation comprend une amplification avec au moins l'une des paires d'amorces sélectionnées parmi SEQ ID N° 1 et 2 ; SEQ ID N° 3 et 4 ; SEQ ID N° 15 et 16 ; SEQ ID N° 17 et 18, SEQ ID N° 19 et 20 ; SEQ ID N° 21 et 22 ; SEQ ID N° 23 et 24 ; SEQ ID N° 29 et 30, et leurs paires d'amorces orthologues ou paralogues, de préférence SEQ ID N° 17 et 18 et ses paires d'amorces orthologues ou paralogues.
  4. Procédé selon la revendication 2 ou 3, dans lequel ladite analyse de l'état de méthylation comprend le fait d'analyser l'état de méthylation d'au moins une position CpG sélectionnée parmi le groupe constitué des positions 38, 74, 90, 124, 151, 156, 205, 224, 228 , 236, 298, et 368 de l'amplicon comme amplifié par la paire d'amorces SEQ ID N° 1 et 2, les positions 158, 180, 308, 344, 360, 394, 421, et 426 de l'amplicon comme amplifié par la paire d'amorces SEQ ID N° 3 et 4, les positions 37, 69, 311, 315, 319, 338 et 371 de l'amplicon comme amplifié par la paire d'amorces SEQ ID N° 5 et 6, les positions 93, 170, 173, 176, et 281 de l'amplicon comme amplifié par la paire d'amorces SEQ ID N° 7 et 8, et leurs positions CpG orthologues ou paralogues.
  5. Procédé selon la revendication 4, dans lequel ladite analyse de l'état de méthylation comprend le fait d'analyser l'état de méthylation d'au moins une position CpG sélectionnée parmi le groupe se composant des positions 38, 74, 90, 124, 156, 205, 224, 236, 298, et 368 de l'amplicon comme amplifié par la paire d'amorces SEQ ID N° 1 et 2, des positions 180, 308, 344, et 394 de l'amplicon comme amplifié par la paire d'amorces SEQ ID N° 3 et 4, et de leurs positions CpG orthologues ou paralogues.
  6. Procédé selon l'une des revendications 1 à 5, dans lequel ladite analyse de l'état de méthylation comprend un procédé sélectionné parmi les digestés enzymatiques spécifiques de méthylation, le séquençage au bisulfite, le MSP, le HeavyMethyl, le MethyLight, le Ms-SNuPE ou d'autres procédés reposant sur une détection d'ADN amplifié.
  7. Procédé selon l'une des revendications 1 à 6, dans lequel ledit mammifère est une souris, un rat, un singe ou un être humain.
  8. Procédé selon l'une des revendications 1 à 7, comprenant en outre une induction avec un TGF-β.
  9. Procédé in vitro pour identifier des substances chimiques et/ou biologiques qui modulent l'expression Foxp3 dans une cellule T, comprenant le fait de mettre une ou plusieurs de ladite substance chimique et/ou biologique en contact avec une cellule T, d'effectuer le procédé selon l'une des revendications 1 à 8, et de détecter, si ladite substance chimique et/ou biologique module la méthylation des positions CpG comme analysé.
  10. Procédé pour identifier des substances chimiques et/ou biologiques selon la revendication 9, dans lequel ladite substance fournit une déméthylation des positions CpG comme analysé à au moins 80%, de préférence 90%, et de manière plus préférable 95%.
  11. Kit pour identifier des cellules T régulatrices sur la base de l'analyse de l'état de méthylation des positions CpG dans le gène Foxp3, comprenant un réactif bisulfite, des protocoles de procédure et des sondes oligonucléotidiques pour l'analyse de méthylation des positions CpG sélectionnées parmi les positions comprenant les positions 38, 74, 90, 124, 156, 205, 224, 236, 298, et 368 de l'amplicon comme amplifié par la paire d'amorces SEQ ID N° 1 et 2, les positions 180, 308, 344, et 394 de l'amplicon comme amplifié par la paire d'amorces SEQ ID N° 3 et 4, et leurs positions CpG orthologues ou paralogues.
  12. Utilisation d'un kit selon la revendication 11 pour la détection et/ou l'identification de cellules T régulatrices CD25+CD4+ stables FoxP3+.
EP07004186A 2006-02-28 2007-02-28 Détection et contrôle de la qualité de lymphocytes T de régulation via l'analyse de méthylation de l'ADN du gène FoxP3 Active EP1826279B1 (fr)

Priority Applications (2)

Application Number Priority Date Filing Date Title
PL07004186T PL1826279T3 (pl) 2006-02-28 2007-02-28 Wykrywanie i kontrola jakości regulatorowych limfocytów T dzięki analizie metylacji DNA genu FoxP3
SI200730679T SI1826279T1 (sl) 2006-02-28 2007-02-28 Zaznavanje in kvalitetna kontrola regulatornih T celic preko DNK-metilacijske analize FoxP3 gena

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
US77763106P 2006-02-28 2006-02-28

Publications (2)

Publication Number Publication Date
EP1826279A1 EP1826279A1 (fr) 2007-08-29
EP1826279B1 true EP1826279B1 (fr) 2011-05-04

Family

ID=38039185

Family Applications (2)

Application Number Title Priority Date Filing Date
EP07004137A Ceased EP1826278A1 (fr) 2006-02-28 2007-02-28 Modification épigénétique des loci pour camta1 et/ou foxp3 à des fins de marquage dans le traitement du cancer
EP07004186A Active EP1826279B1 (fr) 2006-02-28 2007-02-28 Détection et contrôle de la qualité de lymphocytes T de régulation via l'analyse de méthylation de l'ADN du gène FoxP3

Family Applications Before (1)

Application Number Title Priority Date Filing Date
EP07004137A Ceased EP1826278A1 (fr) 2006-02-28 2007-02-28 Modification épigénétique des loci pour camta1 et/ou foxp3 à des fins de marquage dans le traitement du cancer

Country Status (8)

Country Link
US (2) US20070243161A1 (fr)
EP (2) EP1826278A1 (fr)
AT (1) ATE508207T1 (fr)
DE (1) DE602007014278D1 (fr)
DK (1) DK1826279T3 (fr)
ES (1) ES2367012T3 (fr)
PL (1) PL1826279T3 (fr)
SI (1) SI1826279T1 (fr)

Families Citing this family (34)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2280084B1 (fr) * 2004-12-02 2015-02-11 Epigenomics AG Procédés et acides nucléiques pour l'analyse de l'expression génétique associée au pronostic de troubles prolifératifs de cellules prostatiques
ATE508207T1 (de) * 2006-02-28 2011-05-15 Charite Universitaetsmedizin Nachweis und qualitätskontrolle von regulator-t- zellen mittels dna-methylierungsanalyse des foxp3-gens
US20090317810A1 (en) * 2006-04-17 2009-12-24 Epigenomics Ag Methods and nucleic acids for the detection of colorectal cell proliferative disorders
US20090203011A1 (en) * 2007-01-19 2009-08-13 Epigenomics Ag Methods and nucleic acids for analyses of cell proliferative disorders
WO2009059327A2 (fr) * 2007-11-02 2009-05-07 University Of Southern California (Usc) Compositions et procédés comprenant de biomarqueurs de qualité du sperme, de qualité et de fertilité d'une semence
AU2008334901A1 (en) * 2007-12-11 2009-06-18 Epigenomics Ag Methods and nucleic acids for analyses of lung carcinoma
JP2011519271A (ja) * 2008-04-11 2011-07-07 ユニバーシティ オブ サザン カリフォルニア エクスビボで制御性ｔ細胞の作成を加速するための方法および組成物
EP2141245A1 (fr) * 2008-07-03 2010-01-06 Ivana Türbachova Analyse des lymphocytes T de régulation par analyse de méthylation de l'ADN de la région TSDR du gène foxP3
EP2321431A2 (fr) * 2008-07-15 2011-05-18 Epigenomics AG Procédés et acides nucléiques pour l analyse de troubles prolifératifs cellulaires
WO2010037001A2 (fr) 2008-09-26 2010-04-01 Immune Disease Institute, Inc. Oxydation sélective de 5-méthylcytosine par des protéines de la famille tet
US20100124747A1 (en) * 2008-11-03 2010-05-20 University Of Southern California Compositions and methods for diagnosis or prognosis of testicular cancer
DK2199411T3 (en) 2008-12-16 2015-08-03 Epiontis Gmbh Epigenetic markers for the identification of CD3-positive T lymphocytes
US20170233807A1 (en) * 2008-12-16 2017-08-17 Epiontis Gmbh Epigenetic Markers for the Identification of Blood Sub-cells of Type 1
EP2248913B1 (fr) 2009-04-28 2016-10-05 Epiontis GmbH GNLY marqueur épigénétique pour l'identification de cellules tueuses naturelles exprimant CD56
JP5706913B2 (ja) * 2009-12-16 2015-04-22 日立化成株式会社 攻撃的及び防御的免疫マーカーのｅｘｖｉｖｏ誘導により宿主免疫機能を特徴付けるための方法
WO2012045888A1 (fr) 2010-10-08 2012-04-12 Epiontis Gmbh Méthode de détermination du pronostic de survie d'un patient atteint de cancer basée sur l'analyse des lymphocytes t globaux infiltrant la tumeur
US20140178348A1 (en) 2011-05-25 2014-06-26 The Regents Of The University Of California Methods using DNA methylation for identifying a cell or a mixture of cells for prognosis and diagnosis of diseases, and for cell remediation therapies
EP2714933A4 (fr) * 2011-05-25 2014-12-31 Univ Brown Procédés faisant appel à la méthylation de l'adn pour identifier une cellule ou un mélange de cellules afin de pronostiquer et de diagnostiquer des maladies et pour effectuer des traitements de réparation cellulaire
EP2788510B1 (fr) 2012-03-12 2016-12-14 Epiontis GmbH Marqueur épigénétique pour l'identification des lymphocytes t cd3+cd4+
GB201221133D0 (en) 2012-11-23 2013-01-09 Epiontis Gmbh Epigenetic method for the identification of subpopulations of CD8 and T lympocytes, in particular CD8 alpha and beta T lymphocytes
WO2015006811A2 (fr) * 2013-07-19 2015-01-22 The Walter And Eliza Hall Institute Of Medical Research Méthodes de diagnostic
WO2016060278A1 (fr) * 2014-10-17 2016-04-21 国立大学法人東北大学 Procédé d'estimation de sensibilité à une pharmacothérapie contre le cancer colorectal
DK3029150T3 (en) * 2014-12-05 2018-12-10 Epiontis Gmbh Epigenetic method for the identification of follicular T helper cells (TFH cells)
JP6624704B2 (ja) 2015-08-31 2019-12-25 日立化成株式会社 尿路上皮疾患の評価のための分子法
GB201516975D0 (en) * 2015-09-25 2015-11-11 Epiontis Gmbh PARK2 as epigenetic marker for the identification of immune cells, in particular monocytes
GB201516971D0 (en) * 2015-09-25 2015-11-11 Epiontis Gmbh MVD as epigenetic marker for the identification of immune cells, in particular CD56+ NK cells
GB201516972D0 (en) * 2015-09-25 2015-11-11 Epiontis Gmbh LRP5 as epigenetic marker for the identification of immune cells, in particular B-cells
US20170253927A1 (en) * 2016-03-01 2017-09-07 Washington State University Heritable epigenetic modifications as markers of chemotherapy exposure
CN107301330A (zh) * 2017-06-02 2017-10-27 西安电子科技大学 一种利用全基因组数据挖掘甲基化模式的方法
CN107236805A (zh) * 2017-06-22 2017-10-10 深圳市龙岗区疾病预防控制中心（深圳市龙岗区卫生检验中心） 基于亚硫酸氢盐测序法的foxp3基因甲基化检测方法
US12247258B2 (en) 2018-07-05 2025-03-11 Precision For Medicine Gmbh Epigenetic method to detect and distinguish IPEX and IPEX-like syndromes, in particular in newborns
WO2022015860A1 (fr) * 2020-07-15 2022-01-20 Rutgers, The State University Of New Jersey Biomarqueurs permettant d'identifier des patients présentant un risque élevé de progression d'un œsophage de barrett à un adénocarcinome œsophagien
US20250283175A1 (en) * 2021-01-14 2025-09-11 Loma Linda University Methods for evaluation of early stage oral squamous cell carcinoma
DE102023112426A1 (de) * 2023-05-11 2024-11-14 Miltenyi Biotec B.V. & Co. KG Verfahren zur Optimierung von T-Zell - Produkten

Family Cites Families (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20040067491A1 (en) 2000-04-06 2004-04-08 Alexander Olek Diagnosis of diseases associated with metabolism
AU2002224328A1 (en) 2000-09-20 2002-04-02 Case Western Reserve University Methods and compositions for detecting cancers associated with methylation of hmlh1promoter dna
US7662549B1 (en) * 2000-10-27 2010-02-16 The University Of Southern California Methylation altered DNA sequences as markers associated with human cancer
JP2002171973A (ja) 2000-12-07 2002-06-18 Univ Tokyo Ｄｎａメチル化パターンによる細胞の同定法
ATE405586T1 (de) 2001-05-08 2008-09-15 Darwin Molecular Corp Verfahren zur regulierung der immunfunktion in primaten unter verwendung des foxp3-proteins
US20040072197A1 (en) * 2001-11-08 2004-04-15 Jones Peter A. Assay for the detection and quantitation of hemimethylation
AU2003285586A1 (en) 2002-12-03 2004-06-23 Medical Research Council Regulatory t-cells
US20060024676A1 (en) 2003-04-14 2006-02-02 Karen Uhlmann Method of detecting epigenetic biomarkers by quantitative methyISNP analysis
GB0402051D0 (en) * 2004-01-29 2004-03-03 Metcalfe Su Fate determination in immunity
WO2005118872A2 (fr) 2004-06-01 2005-12-15 The Regents Of The University Of Michigan Méthodes et équipements de diagnostic ou de contrôle des maladies autoimmunes et des pathologies inflammatoires chroniques
ATE508207T1 (de) 2006-02-28 2011-05-15 Charite Universitaetsmedizin Nachweis und qualitätskontrolle von regulator-t- zellen mittels dna-methylierungsanalyse des foxp3-gens

Also Published As

Publication number Publication date
ATE508207T1 (de) 2011-05-15
US10876163B2 (en) 2020-12-29
ES2367012T3 (es) 2011-10-27
EP1826278A1 (fr) 2007-08-29
PL1826279T3 (pl) 2011-11-30
US20070243161A1 (en) 2007-10-18
EP1826279A1 (fr) 2007-08-29
DE602007014278D1 (de) 2011-06-16
SI1826279T1 (sl) 2011-10-28
US20070269823A1 (en) 2007-11-22
DK1826279T3 (da) 2011-09-05

Similar Documents

Publication Publication Date Title
EP1826279B1 (fr) Détection et contrôle de la qualité de lymphocytes T de régulation via l'analyse de méthylation de l'ADN du gène FoxP3
EP2199411B1 (fr) Marqueurs épigénétiques pour l'identification des lymphocytes T CD3+
US10590475B2 (en) Detection of immune cells, in particular T cells through DNA-methylation analysis of the genes CCR6 and BLR1
Das et al. DNMT1 and AIM1 Imprinting in human placenta revealed through a genome-wide screen for allele-specific DNA methylation
CA2864192C (fr) Marqueur epigenetique pour l'identification des lymphocytes t cd3+cd4+
US9096900B2 (en) Epigenetic marker for the identification of natural killer cells
EP3353319B1 (fr) Utilisation de park2 en tant que marqueur épigénétique pour l'identification de cellules immunitaires, en particulier les monocytes
US10294527B2 (en) Epigenetic marker for the identification of natural killer cells
EP3029150B1 (fr) Procédé épigénétique pour l'identification de lymphocites T-auxiliaires- folliculaires
US12286675B2 (en) Epigenetic markers for the identification of blood sub-cells of type 1
EP3669000B1 (fr) L'endosialine (cd248) comme marqueur épigénétique pour l'identification de cellules immunitaires, en particulier de lymphocytes t cd8+ naïves
US9556484B2 (en) Epigenetic marker for the identification of IL17 positive T cells in complex samples
HK1257582B (en) Park2 as epigenetic marker for the identification of immune cells, in particular monocytes
HK1163189B (en) Epigenetic markers for the identification of cd3 positive t-lymphocytes

Legal Events

Date Code Title Description
PUAI Public reference made under article 153(3) epc to a published international application that has entered the european phase

Free format text: ORIGINAL CODE: 0009012

AK Designated contracting states

Kind code of ref document: A1

Designated state(s): AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI SK TR

AX Request for extension of the european patent

Extension state: AL BA HR MK YU

17P Request for examination filed

Effective date: 20080215

17Q First examination report despatched

Effective date: 20080314

AKX Designation fees paid

Designated state(s): AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI SK TR

GRAP Despatch of communication of intention to grant a patent

Free format text: ORIGINAL CODE: EPIDOSNIGR1

GRAS Grant fee paid

Free format text: ORIGINAL CODE: EPIDOSNIGR3

GRAA (expected) grant

Free format text: ORIGINAL CODE: 0009210

AK Designated contracting states

Kind code of ref document: B1

Designated state(s): AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI SK TR

REG Reference to a national code

Ref country code: GB

Ref legal event code: FG4D

REG Reference to a national code

Ref country code: CH

Ref legal event code: EP

REG Reference to a national code

Ref country code: IE

Ref legal event code: FG4D

REF Corresponds to:

Ref document number: 602007014278

Country of ref document: DE

Date of ref document: 20110616

Kind code of ref document: P

REG Reference to a national code

Ref country code: DE

Ref legal event code: R096

Ref document number: 602007014278

Country of ref document: DE

Effective date: 20110616

REG Reference to a national code

Ref country code: SE

Ref legal event code: TRGR

REG Reference to a national code

Ref country code: DK

Ref legal event code: T3

REG Reference to a national code

Ref country code: NL

Ref legal event code: T3

REG Reference to a national code

Ref country code: CH

Ref legal event code: NV

Representative=s name: E. BLUM & CO. AG PATENT- UND MARKENANWAELTE VSP

REG Reference to a national code

Ref country code: ES

Ref legal event code: FG2A

Ref document number: 2367012

Country of ref document: ES

Kind code of ref document: T3

Effective date: 20111027

PG25 Lapsed in a contracting state [announced via postgrant information from national office to epo]

Ref country code: PT

Free format text: LAPSE BECAUSE OF FAILURE TO SUBMIT A TRANSLATION OF THE DESCRIPTION OR TO PAY THE FEE WITHIN THE PRESCRIBED TIME-LIMIT

Effective date: 20110905

PG25 Lapsed in a contracting state [announced via postgrant information from national office to epo]

Ref country code: FI

Free format text: LAPSE BECAUSE OF FAILURE TO SUBMIT A TRANSLATION OF THE DESCRIPTION OR TO PAY THE FEE WITHIN THE PRESCRIBED TIME-LIMIT

Effective date: 20110504

Ref country code: CY

Free format text: LAPSE BECAUSE OF FAILURE TO SUBMIT A TRANSLATION OF THE DESCRIPTION OR TO PAY THE FEE WITHIN THE PRESCRIBED TIME-LIMIT

Effective date: 20110504

Ref country code: GR

Free format text: LAPSE BECAUSE OF FAILURE TO SUBMIT A TRANSLATION OF THE DESCRIPTION OR TO PAY THE FEE WITHIN THE PRESCRIBED TIME-LIMIT

Effective date: 20110805

REG Reference to a national code

Ref country code: PL

Ref legal event code: T3

REG Reference to a national code

Ref country code: SK

Ref legal event code: T3

Ref document number: E 10066

Country of ref document: SK

REG Reference to a national code

Ref country code: HU

Ref legal event code: AG4A

Ref document number: E012047

Country of ref document: HU

PG25 Lapsed in a contracting state [announced via postgrant information from national office to epo]

Ref country code: EE

Free format text: LAPSE BECAUSE OF FAILURE TO SUBMIT A TRANSLATION OF THE DESCRIPTION OR TO PAY THE FEE WITHIN THE PRESCRIBED TIME-LIMIT

Effective date: 20110504

PG25 Lapsed in a contracting state [announced via postgrant information from national office to epo]

Ref country code: RO

Free format text: LAPSE BECAUSE OF FAILURE TO SUBMIT A TRANSLATION OF THE DESCRIPTION OR TO PAY THE FEE WITHIN THE PRESCRIBED TIME-LIMIT

Effective date: 20110504

PLBE No opposition filed within time limit

Free format text: ORIGINAL CODE: 0009261

STAA Information on the status of an ep patent application or granted ep patent

Free format text: STATUS: NO OPPOSITION FILED WITHIN TIME LIMIT

26N No opposition filed

Effective date: 20120207

REG Reference to a national code

Ref country code: DE

Ref legal event code: R097

Ref document number: 602007014278

Country of ref document: DE

Effective date: 20120207

PG25 Lapsed in a contracting state [announced via postgrant information from national office to epo]

Ref country code: BG

Free format text: LAPSE BECAUSE OF FAILURE TO SUBMIT A TRANSLATION OF THE DESCRIPTION OR TO PAY THE FEE WITHIN THE PRESCRIBED TIME-LIMIT

Effective date: 20110804

PGFP Annual fee paid to national office [announced via postgrant information from national office to epo]

Ref country code: LT

Payment date: 20150213

Year of fee payment: 9

Ref country code: HU

Payment date: 20150213

Year of fee payment: 9

PGFP Annual fee paid to national office [announced via postgrant information from national office to epo]

Ref country code: LV

Payment date: 20150224

Year of fee payment: 9

REG Reference to a national code

Ref country code: FR

Ref legal event code: PLFP

Year of fee payment: 10

REG Reference to a national code

Ref country code: LT

Ref legal event code: MM4D

Effective date: 20160228

PG25 Lapsed in a contracting state [announced via postgrant information from national office to epo]

Ref country code: LT

Free format text: LAPSE BECAUSE OF NON-PAYMENT OF DUE FEES

Effective date: 20160228

Ref country code: HU

Free format text: LAPSE BECAUSE OF NON-PAYMENT OF DUE FEES

Effective date: 20160301

PG25 Lapsed in a contracting state [announced via postgrant information from national office to epo]

Ref country code: LV

Free format text: LAPSE BECAUSE OF NON-PAYMENT OF DUE FEES

Effective date: 20160228

REG Reference to a national code

Ref country code: FR

Ref legal event code: PLFP

Year of fee payment: 11

REG Reference to a national code

Ref country code: FR

Ref legal event code: PLFP

Year of fee payment: 12

PGFP Annual fee paid to national office [announced via postgrant information from national office to epo]

Ref country code: ES

Payment date: 20200320

Year of fee payment: 14

Ref country code: NL

Payment date: 20200323

Year of fee payment: 14

Ref country code: SE

Payment date: 20200325

Year of fee payment: 14

Ref country code: MC

Payment date: 20200323

Year of fee payment: 14

Ref country code: PL

Payment date: 20200319

Year of fee payment: 14

Ref country code: IE

Payment date: 20200323

Year of fee payment: 14

Ref country code: IT

Payment date: 20200325

Year of fee payment: 14

Ref country code: DK

Payment date: 20200323

Year of fee payment: 14

Ref country code: AT

Payment date: 20200319

Year of fee payment: 14

PGFP Annual fee paid to national office [announced via postgrant information from national office to epo]

Ref country code: SI

Payment date: 20200317

Year of fee payment: 14

Ref country code: BE

Payment date: 20200323

Year of fee payment: 14

Ref country code: SK

Payment date: 20200323

Year of fee payment: 14

Ref country code: CZ

Payment date: 20200319

Year of fee payment: 14

Ref country code: LU

Payment date: 20200323

Year of fee payment: 14

Ref country code: IS

Payment date: 20200319

Year of fee payment: 14

PGFP Annual fee paid to national office [announced via postgrant information from national office to epo]

Ref country code: TR

Payment date: 20200320

Year of fee payment: 14

REG Reference to a national code

Ref country code: DK

Ref legal event code: EBP

Effective date: 20210228

PG25 Lapsed in a contracting state [announced via postgrant information from national office to epo]

Ref country code: MC

Free format text: LAPSE BECAUSE OF NON-PAYMENT OF DUE FEES

Effective date: 20210301

REG Reference to a national code

Ref country code: AT

Ref legal event code: MM01

Ref document number: 508207

Country of ref document: AT

Kind code of ref document: T

Effective date: 20210228

REG Reference to a national code

Ref country code: BE

Ref legal event code: MM

Effective date: 20210228

Ref country code: SK

Ref legal event code: MM4A

Ref document number: E 10066

Country of ref document: SK

Effective date: 20210228

PG25 Lapsed in a contracting state [announced via postgrant information from national office to epo]

Ref country code: CZ

Free format text: LAPSE BECAUSE OF NON-PAYMENT OF DUE FEES

Effective date: 20210228

Ref country code: LU

Free format text: LAPSE BECAUSE OF NON-PAYMENT OF DUE FEES

Effective date: 20210228

Ref country code: AT

Free format text: LAPSE BECAUSE OF NON-PAYMENT OF DUE FEES

Effective date: 20210228

PG25 Lapsed in a contracting state [announced via postgrant information from national office to epo]

Ref country code: SK

Free format text: LAPSE BECAUSE OF NON-PAYMENT OF DUE FEES

Effective date: 20210228

REG Reference to a national code

Ref country code: NL

Ref legal event code: MM

Effective date: 20210301

PG25 Lapsed in a contracting state [announced via postgrant information from national office to epo]

Ref country code: NL

Free format text: LAPSE BECAUSE OF NON-PAYMENT OF DUE FEES

Effective date: 20210301

PG25 Lapsed in a contracting state [announced via postgrant information from national office to epo]

Ref country code: SE

Free format text: LAPSE BECAUSE OF NON-PAYMENT OF DUE FEES

Effective date: 20210301

Ref country code: DK

Free format text: LAPSE BECAUSE OF NON-PAYMENT OF DUE FEES

Effective date: 20210228

Ref country code: IE

Free format text: LAPSE BECAUSE OF NON-PAYMENT OF DUE FEES

Effective date: 20210228

REG Reference to a national code

Ref country code: SI

Ref legal event code: KO00

Effective date: 20211201

PG25 Lapsed in a contracting state [announced via postgrant information from national office to epo]

Ref country code: SI

Free format text: LAPSE BECAUSE OF NON-PAYMENT OF DUE FEES

Effective date: 20210301

PG25 Lapsed in a contracting state [announced via postgrant information from national office to epo]

Ref country code: IT

Free format text: LAPSE BECAUSE OF NON-PAYMENT OF DUE FEES

Effective date: 20210228

REG Reference to a national code

Ref country code: ES

Ref legal event code: FD2A

Effective date: 20220513

PG25 Lapsed in a contracting state [announced via postgrant information from national office to epo]

Ref country code: ES

Free format text: LAPSE BECAUSE OF NON-PAYMENT OF DUE FEES

Effective date: 20210301

Ref country code: BE

Free format text: LAPSE BECAUSE OF NON-PAYMENT OF DUE FEES

Effective date: 20210228

REG Reference to a national code

Ref country code: DE

Ref legal event code: R082

Ref document number: 602007014278

Country of ref document: DE

Representative=s name: KRAUSS, JAN, DR., DE

PG25 Lapsed in a contracting state [announced via postgrant information from national office to epo]

Ref country code: PL

Free format text: LAPSE BECAUSE OF NON-PAYMENT OF DUE FEES

Effective date: 20210228

P01 Opt-out of the competence of the unified patent court (upc) registered

Effective date: 20230525

PG25 Lapsed in a contracting state [announced via postgrant information from national office to epo]

Ref country code: TR

Free format text: LAPSE BECAUSE OF NON-PAYMENT OF DUE FEES

Effective date: 20210228

PGFP Annual fee paid to national office [announced via postgrant information from national office to epo]

Ref country code: DE

Payment date: 20250218

Year of fee payment: 19

PGFP Annual fee paid to national office [announced via postgrant information from national office to epo]

Ref country code: CH

Payment date: 20250301

Year of fee payment: 19

PGFP Annual fee paid to national office [announced via postgrant information from national office to epo]

Ref country code: FR

Payment date: 20250220

Year of fee payment: 19

PGFP Annual fee paid to national office [announced via postgrant information from national office to epo]

Ref country code: GB

Payment date: 20250220

Year of fee payment: 19

PG25 Lapsed in a contracting state [announced via postgrant information from national office to epo]

Ref country code: IS

Free format text: LAPSE BECAUSE OF NON-PAYMENT OF DUE FEES

Effective date: 20210906